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The player, controlling a ninja, must fight his way through various levels populated by opponents, collecting necessary items in the process. Each level depicts a different locale and is divided into several screens. The game is presented in an isometric view and the ninja can move in four different directions and jump.

Enemies, armed with fists and various ninja weapons, wander around the levels. The ninja must fight them either bare-handed or with the weaponry he finds along the way; in either case, he has a number of blows and attacks at his disposal, as well as the ability to block. There is a special weapon, shuriken, which are thrown in a straight line rather than used for melee combat; if they strike an enemy, they will instantly kill or at least severely damage them.

Various items scattered around the levels, such as keys, a rope and a map; collecting these items and using them in a proper place is necessary for completing the game. There are also hot-dogs that restore health when eaten.

The game continues from the aftermath of the events of The Last Ninja. With the Koga scrolls now in his possession, Armakuni has begun training a new order of shadow warriors. During a training session, he is mysteriously transported to 20th-century New York City. Torn from his own time, Armakuni must defeat the evil shogun Kunitoki once more.

Last Ninja 2 was an enormous commercial success. According to System 3's Mark Cale, 5.5 million copies were sold for the Commodore 64 version alone; at that time, the user base of the C64 was estimated at 20 million, meaning that one in four C64 owners bought the game.[2]